Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies
Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies
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DOI：
10.1089/cmb.2009.0238
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发表时间：
2010-11-01
影响因子：
1.7
通讯作者：
Corbeil, Jacques
中科院分区：
文献类型：
--
作者：
Boisvert, Sebastien;Laviolette, Francois;Corbeil, Jacques
对于基因组研究而言，获得目标物种准确的基因组序列现在是一个先决条件。获得高质量基因组序列的一个重要步骤是将短读段正确且准确地组装成能代表连续基因组区域的较长序列。当前的测序技术不断提高通量，同时相应地降低成本和缩短时间。不幸的是，获得大量读段的好处因测序错误而变得复杂，并且每个平台都存在不同的偏差。尽管有软件可用于对每个单独系统的读段进行组装，但尚未有人提出基于来自不同技术混合读段进行高质量同时组装的方法。在本文中，我们描述了一种并行短读段组装程序，称为Ray，它是为组装从多种测序平台组合获得的读段而开发的。我们在模拟数据集和真实数据集上比较了它与其他组装程序的性能。我们使用罗氏/454和 Illumina读段的组合来组装三个不同的基因组。我们表明，混合测序技术有系统地减少了重叠群的数量和错误数量。由于其开放性，这个新工具有望作为开发一种可通用的组装程序的基础（可获取网址：http://deNovoAssembler.sf.Net/）。如需在线补充材料，请访问www.liebertonline.com。
An accurate genome sequence of a desired species is now a pre-requisite for genome research. An important step in obtaining a high-quality genome sequence is to correctly assemble short reads into longer sequences accurately representing contiguous genomic regions. Current sequencing technologies continue to offer increases in throughput, and corresponding reductions in cost and time. Unfortunately, the benefit of obtaining a large number of reads is complicated by sequencing errors, with different biases being observed with each platform. Although software are available to assemble reads for each individual system, no procedure has been proposed for high-quality simultaneous assembly based on reads from a mix of different technologies. In this paper, we describe a parallel short-read assembler, called Ray, which has been developed to assemble reads obtained from a combination of sequencing platforms. We compared its performance to other assemblers on simulated and real datasets. We used a combination of Roche/454 and Illumina reads to assemble three different genomes. We showed that mixing sequencing technologies systematically reduces the number of contigs and the number of errors. Because of its open nature, this new tool will hopefully serve as a basis to develop an assembler that can be of universal utilization (availability: http://deNovoAssembler.sf.Net/). For online Supplementary Material, see www.liebertonline.com.